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Fix new UP031 errors raised by ruff 0.0.262

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This commit is contained in:
Nicola Soranzo
2023-05-03 17:57:06 +01:00
parent e6d09a9ba0
commit c210257e0d
34 changed files with 165 additions and 170 deletions
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lib/galaxy/datatypes/blast.py
+1 -2
View File
@@ -173,8 +173,7 @@ class BlastXml(GenericXml):
# Enough to check <BlastOutput_program> and <BlastOutput_version> match
h.close()
raise ValueError(
"BLAST XML headers don't match for %s and %s - have:\n%s\n...\n\nAnd:\n%s\n...\n"
% (split_files[0], f, old_header[:300], header[:300])
f"BLAST XML headers don't match for {split_files[0]} and {f} - have:\n{old_header[:300]}\n...\n\nAnd:\n{header[:300]}\n...\n"
)
else:
out.write(" <Iteration>\n")
lib/galaxy/datatypes/registry.py
+3 -2
View File
@@ -237,8 +237,9 @@ class Registry:
# Because of the way that the value of can_process_datatype was set above, we know that the value of
# override is True.
self.log.debug(
"Overriding conflicting datatype with extension '%s', using datatype from %s."
% (str(extension), str(config))
"Overriding conflicting datatype with extension '%s', using datatype from %s.",
extension,
config,
)
if make_subclass:
datatype_class = type(datatype_class_name, (datatype_class,), {})
lib/galaxy/datatypes/sequence.py
+1 -2
View File
@@ -277,8 +277,7 @@ class Sequence(data.Text):
start_chunk = -1
# extract, unzip, trim, recompress
result.append(
"(dd bs=1 skip=%s count=%s if=%s 2> /dev/null )| zcat | ( tail -n +%s 2> /dev/null) | head -%s | gzip -c >> %s"
% (
"(dd bs=1 skip={} count={} if={} 2> /dev/null )| zcat | ( tail -n +{} 2> /dev/null) | head -{} | gzip -c >> {}".format(
start_copy,
end_copy - start_copy,
input_name,
lib/galaxy/datatypes/spaln.py
+4 -4
View File
@@ -71,8 +71,9 @@ class _SpalnDb(Data):
opt_text = ""
if composite_file.get("description"):
rval.append(
'<li><a href="%s" type="application/binary">%s (%s)</a>%s</li>'
% (fn, fn, composite_file.get("description"), opt_text)
'<li><a href="{}" type="application/binary">{} ({})</a>{}</li>'.format(
fn, fn, composite_file.get("description"), opt_text
)
)
else:
rval.append(f'<li><a href="{fn}" type="application/binary">{fn}</a>{opt_text}</li>')
@@ -86,8 +87,7 @@ class _SpalnDb(Data):
efp = dataset.extra_files_path
flist = os.listdir(efp)
rval = [
"<html><head><title>Files for Composite Dataset %s</title></head><body><p/>Composite %s contains:<p/><ul>"
% (dataset.name, dataset.name)
f"<html><head><title>Files for Composite Dataset {dataset.name}</title></head><body><p/>Composite {dataset.name} contains:<p/><ul>"
]
for fname in flist:
sfname = os.path.split(fname)[-1]
lib/galaxy/dependencies/pinned-lint-requirements.txt
+1 -1
View File
@@ -5,6 +5,6 @@ importlib-metadata==4.2.0
mccabe==0.7.0
pycodestyle==2.9.1
pyflakes==2.5.0
ruff==0.0.261
ruff==0.0.264
typing_extensions==4.5.0
zipp==3.15.0
lib/galaxy/jobs/__init__.py
+6 -4
View File
@@ -1887,8 +1887,9 @@ class MinimalJobWrapper(HasResourceParameters):
# and when the job is recovered, it won't be found.
if os.path.exists(dataset_path.real_path) and os.stat(dataset_path.real_path).st_size > 0:
log.warning(
"finish(): %s not found, but %s is not empty, so it will be used instead"
% (dataset_path.false_path, dataset_path.real_path)
"finish(): %s not found, but %s is not empty, so it will be used instead",
dataset_path.false_path,
dataset_path.real_path,
)
else:
# Prior to fail we need to set job.state
@@ -2160,8 +2161,9 @@ class MinimalJobWrapper(HasResourceParameters):
)
return (
JobState.runner_states.GLOBAL_WALLTIME_REACHED,
"Job ran longer than the maximum allowed execution time (runtime: %s, limit: %s), please try different inputs or parameters"
% (str(runtime).split(".")[0], self.app.job_config.limits.walltime),
"Job ran longer than the maximum allowed execution time (runtime: {}, limit: {}), please try different inputs or parameters".format(
str(runtime).split(".")[0], self.app.job_config.limits.walltime
),
)
return None
lib/galaxy/model/security.py
+1 -2
View File
@@ -1342,8 +1342,7 @@ class GalaxyRBACAgent(RBACAgent):
break
else:
raise Exception(
"Invalid class (%s) specified for target_library_item (%s)"
% (target_library_item.__class__, target_library_item.__class__.__name__)
f"Invalid class ({target_library_item.__class__}) specified for target_library_item ({target_library_item.__class__.__name__})"
)
# Make sure user's private role is included
private_role = self.model.security_agent.get_private_user_role(user)
lib/galaxy/objectstore/__init__.py
+10 -8
View File
@@ -960,8 +960,7 @@ class NestedObjectStore(BaseObjectStore):
return store.__getattribute__(method)(obj, **kwargs)
if default_is_exception:
raise default(
"objectstore, _call_method failed: %s on %s, kwargs: %s"
% (method, self._repr_object_for_exception(obj), str(kwargs))
f"objectstore, _call_method failed: {method} on {self._repr_object_for_exception(obj)}, kwargs: {kwargs}"
)
else:
return default
@@ -1138,8 +1137,10 @@ class DistributedObjectStore(NestedObjectStore):
)
else:
log.debug(
"Using preferred backend '%s' for creation of %s %s"
% (object_store_id, obj.__class__.__name__, obj.id)
"Using preferred backend '%s' for creation of %s %s",
object_store_id,
obj.__class__.__name__,
obj.id,
)
return self.backends[object_store_id].create(obj, **kwargs)
else:
@@ -1151,8 +1152,7 @@ class DistributedObjectStore(NestedObjectStore):
return self.backends[object_store_id].__getattribute__(method)(obj, **kwargs)
if default_is_exception:
raise default(
"objectstore, _call_method failed: %s on %s, kwargs: %s"
% (method, self._repr_object_for_exception(obj), str(kwargs))
f"objectstore, _call_method failed: {method} on {self._repr_object_for_exception(obj)}, kwargs: {kwargs}"
)
else:
return default
@@ -1178,8 +1178,10 @@ class DistributedObjectStore(NestedObjectStore):
return obj.object_store_id
else:
log.warning(
"The backend object store ID (%s) for %s object with ID %s is invalid"
% (obj.object_store_id, obj.__class__.__name__, obj.id)
"The backend object store ID (%s) for %s object with ID %s is invalid",
obj.object_store_id,
obj.__class__.__name__,
obj.id,
)
elif self.search_for_missing:
# if this instance has been switched from a non-distributed to a
lib/galaxy/tool_shed/galaxy_install/install_manager.py
+1 -4
View File
@@ -101,10 +101,7 @@ class InstallRepositoryManager:
repository_revision_dict: RepositoryMetadataInstallInfoDict = items[1]
repo_info_dict: ExtraRepoInfo = items[2]
else:
message = (
"Unable to retrieve installation information from tool shed %s for revision %s of repository %s owned by %s"
% (str(tool_shed_url), str(changeset_revision), str(name), str(owner))
)
message = f"Unable to retrieve installation information from tool shed {tool_shed_url} for revision {changeset_revision} of repository {name} owned by {owner}"
log.warning(message)
raise exceptions.InternalServerError(message)
# Make sure the tool shed returned everything we need for installing the repository.
lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py
+10 -10
View File
@@ -875,14 +875,12 @@ class InstalledRepositoryManager:
if new_dependency_name and new_dependency_type and new_dependency_version:
# Update all attributes of the tool_dependency record in the database.
log.debug(
"Updating version %s of tool dependency %s %s to have new version %s and type %s."
% (
str(tool_dependency.version),
str(tool_dependency.type),
str(tool_dependency.name),
str(new_dependency_version),
str(new_dependency_type),
)
"Updating version %s of tool dependency %s %s to have new version %s and type %s.",
tool_dependency.version,
tool_dependency.type,
tool_dependency.name,
new_dependency_version,
new_dependency_type,
)
tool_dependency.type = new_dependency_type
tool_dependency.version = new_dependency_version
@@ -895,8 +893,10 @@ class InstalledRepositoryManager:
# We have no new tool dependency definition based on a matching dependency name, so remove
# the existing tool dependency record from the database.
log.debug(
"Deleting version %s of tool dependency %s %s from the database since it is no longer defined."
% (str(tool_dependency.version), str(tool_dependency.type), str(tool_dependency.name))
"Deleting version %s of tool dependency %s %s from the database since it is no longer defined.",
tool_dependency.version,
tool_dependency.type,
tool_dependency.name,
)
context.delete(tool_dependency)
context.flush()
lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
+3 -2
View File
@@ -156,8 +156,9 @@ class InstalledRepositoryMetadataManager(MetadataGenerator):
unsuccessful_count += 1
else:
log.debug(
"Successfully reset metadata on repository %s owned by %s"
% (str(repository.name), str(repository.owner))
"Successfully reset metadata on repository %s owned by %s",
repository.name,
repository.owner,
)
successful_count += 1
except Exception:
lib/galaxy/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
+6 -7
View File
@@ -234,15 +234,14 @@ class RepositoryDependencyInstallManager:
install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES,
install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES,
]:
info_msg = (
log.info(
"Skipping installation of revision %s of repository '%s' because it was installed "
% (changeset_revision, repository_db_record.name)
"with the (possibly updated) revision %s and its current installation status is '%s'.",
changeset_revision,
repository_db_record.name,
installed_changeset_revision,
repository_db_record.status,
)
info_msg += (
"with the (possibly updated) revision %s and its current installation status is '%s'."
% (installed_changeset_revision, repository_db_record.status)
)
log.info(info_msg)
can_update_db_record = False
else:
if repository_db_record.status in [
lib/galaxy/tool_shed/galaxy_install/tools/data_manager.py
+6 -4
View File
@@ -135,15 +135,17 @@ class DataManagerHandler:
tool_dict = repository_tools_by_guid.get(tool_guid, None)
if tool_dict is None:
log.error(
"Data manager tool guid '%s' could not be found for '%s'. Perhaps the tool is invalid?"
% (tool_guid, data_manager_id)
"Data manager tool guid '%s' could not be found for '%s'. Perhaps the tool is invalid?",
tool_guid,
data_manager_id,
)
continue
tool = tool_dict.get("tool", None)
if tool is None:
log.error(
"Data manager tool with guid '%s' could not be found for '%s'. Perhaps the tool is invalid?"
% (tool_guid, data_manager_id)
"Data manager tool with guid '%s' could not be found for '%s'. Perhaps the tool is invalid?",
tool_guid,
data_manager_id,
)
continue
tool_config_filename = tool_dict.get("tool_config_filename", None)
lib/galaxy/tool_shed/metadata/metadata_generator.py
+8 -17
View File
@@ -907,10 +907,9 @@ class MetadataGenerator:
# shed may have simply been inaccessible when metadata was being generated for the
# installed tool shed repository.
error_message = (
"Ignoring invalid repository dependency definition for tool shed %s, name %s, owner %s, "
% (toolshed, name, owner)
f"Ignoring invalid repository dependency definition for tool shed {toolshed}, name {name}, owner {owner}, "
f"changeset revision {changeset_revision}."
)
error_message += f"changeset revision {changeset_revision}."
log.debug(error_message)
is_valid = False
return repository_dependency_tup, is_valid, error_message
@@ -925,10 +924,9 @@ class MetadataGenerator:
)
except Exception:
error_message = (
"Ignoring repository dependency definition for tool shed %s, name %s, owner %s, "
% (toolshed, name, owner)
f"Ignoring repository dependency definition for tool shed {toolshed}, name {name}, owner {owner}, "
f"changeset revision {changeset_revision} because the owner is invalid."
)
error_message += f"changeset revision {changeset_revision} because the owner is invalid."
log.debug(error_message)
is_valid = False
return repository_dependency_tup, is_valid, error_message
@@ -945,10 +943,9 @@ class MetadataGenerator:
)
except Exception:
error_message = (
"Ignoring repository dependency definition for tool shed %s, name %s, owner %s, "
% (toolshed, name, owner)
f"Ignoring repository dependency definition for tool shed {toolshed}, name {name}, owner {owner}, "
f"changeset revision {changeset_revision} because the name is invalid. "
)
error_message += f"changeset revision {changeset_revision} because the name is invalid. "
log.debug(error_message)
is_valid = False
return repository_dependency_tup, is_valid, error_message
@@ -980,10 +977,7 @@ class MetadataGenerator:
break
if not found:
error_message = (
"Ignoring repository dependency definition for tool shed %s, name %s, owner %s, "
% (toolshed, name, owner)
)
error_message += (
f"Ignoring repository dependency definition for tool shed {toolshed}, name {name}, owner {owner}, "
f"changeset revision {changeset_revision} because the changeset revision is invalid. "
)
log.debug(error_message)
@@ -993,10 +987,7 @@ class MetadataGenerator:
# Repository dependencies are currently supported within a single tool shed.
error_message = (
"Repository dependencies are currently supported only within the same tool shed. Ignoring "
)
error_message += (
"repository dependency definition for tool shed %s, name %s, owner %s, changeset revision %s. "
% (toolshed, name, owner, changeset_revision)
f"repository dependency definition for tool shed {toolshed}, name {name}, owner {owner}, changeset revision {changeset_revision}. "
)
log.debug(error_message)
is_valid = False
lib/galaxy/tool_shed/util/repository_util.py
+3 -2
View File
@@ -653,8 +653,9 @@ def get_tool_shed_status_for(tool_shed_registry: Registry, repository: ToolShedR
# This should handle backward compatility to the Galaxy 12/20/12 release. We used to only handle updates for an installed revision
# using a boolean value.
log.debug(
"Error attempting to get tool shed status for installed repository %s: %s\nAttempting older 'check_for_updates' method.\n"
% (str(repository.name), str(e))
"Error attempting to get tool shed status for installed repository %s: %s\nAttempting older 'check_for_updates' method.\n",
repository.name,
e,
)
pathspec = ["repository", "check_for_updates"]
params["from_update_manager"] = True
lib/galaxy/tool_util/deps/brew_exts.py
+4 -4
View File
@@ -160,14 +160,14 @@ class CommandLineException(Exception):
self.stdout = stdout
self.stderr = stderr
self.message = (
"Failed to execute command-line %s, stderr was:\n"
"Failed to execute command-line {}, stderr was:\n"
"-------->>begin stderr<<--------\n"
"%s\n"
"{}\n"
"-------->>end stderr<<--------\n"
"-------->>begin stdout<<--------\n"
"%s\n"
"{}\n"
"-------->>end stdout<<--------\n"
) % (command, stderr, stdout)
).format(command, stderr, stdout)
def __str__(self):
return self.message
lib/galaxy/tools/__init__.py
+9 -13
View File
@@ -1608,23 +1608,19 @@ class Tool(Dictifiable):
possible_cases.remove(case.value)
except Exception:
log.debug(
"Tool with id '%s': a when tag has been defined for '%s (%s) --> %s', but does not appear to be selectable."
% (
self.id,
group_c.name,
group_c.test_param.name,
case.value,
)
)
for unspecified_case in possible_cases:
log.warning(
"Tool with id '%s': a when tag has not been defined for '%s (%s) --> %s', assuming empty inputs."
% (
"Tool with id '%s': a when tag has been defined for '%s (%s) --> %s', but does not appear to be selectable.",
self.id,
group_c.name,
group_c.test_param.name,
unspecified_case,
case.value,
)
for unspecified_case in possible_cases:
log.warning(
"Tool with id '%s': a when tag has not been defined for '%s (%s) --> %s', assuming empty inputs.",
self.id,
group_c.name,
group_c.test_param.name,
unspecified_case,
)
case = ConditionalWhen()
case.value = unspecified_case
lib/galaxy/tools/error_reports/plugins/github.py
+5 -6
View File
@@ -13,7 +13,7 @@ log = logging.getLogger(__name__)
class GithubPlugin(BaseGitPlugin):
"""Send error report to Github."""
"""Send error report to GitHub."""
plugin_type = "github"
@@ -23,7 +23,7 @@ class GithubPlugin(BaseGitPlugin):
self.verbose = string_as_bool(kwargs.get("verbose", False))
self.user_submission = string_as_bool(kwargs.get("user_submission", False))
# Github settings
# GitHub settings
self.github_base_url = kwargs.get("github_base_url", "https://github.com")
self.github_api_url = kwargs.get("github_api_url", "https://api.github.com")
self.git_default_repo_owner = kwargs.get("github_default_repo_owner", False)
@@ -46,7 +46,7 @@ class GithubPlugin(BaseGitPlugin):
self.label_cache["default"] = {}
self._fill_label_cache(repo, "default")
except ImportError:
log.error("Please install pygithub to submit bug reports to github")
log.error("Please install pygithub to submit bug reports to GitHub")
self.github = None
def submit_report(self, dataset, job, tool, **kwargs):
@@ -99,9 +99,8 @@ class GithubPlugin(BaseGitPlugin):
else:
self._append_issue(issue_cache_key, error_title, error_message)
return (
'Submitted error report to Github. Your issue number is <a href="%s/%s/issues/%s" '
'target="_blank">#%s</a>.'
% (
'Submitted error report to GitHub. Your issue number is <a href="{}/{}/issues/{}" '
'target="_blank">#{}</a>.'.format(
self.github_base_url,
github_projecturl,
self.issue_cache[issue_cache_key][error_title].number,
lib/galaxy/tools/error_reports/plugins/gitlab.py
+2 -3
View File
@@ -185,9 +185,8 @@ class GitLabPlugin(BaseGitPlugin):
)
return (
'Submitted error report to GitLab. Your issue number is <a href="%s/%s/issues/%s" '
'target="_blank">#%s</a>.'
% (
'Submitted error report to GitLab. Your issue number is <a href="{}/{}/issues/{}" '
'target="_blank">#{}</a>.'.format(
self.gitlab_base_url,
gitlab_projecturl,
self.issue_cache[issue_cache_key][error_title],
lib/galaxy/util/commands.py
+4 -4
View File
@@ -155,14 +155,14 @@ class CommandLineException(Exception):
self.stderr = stderr
self.returncode = returncode
self.message = (
"Failed to execute command-line %s, stderr was:\n"
"Failed to execute command-line {}, stderr was:\n"
"-------->>begin stderr<<--------\n"
"%s\n"
"{}\n"
"-------->>end stderr<<--------\n"
"-------->>begin stdout<<--------\n"
"%s\n"
"{}\n"
"-------->>end stdout<<--------\n"
) % (command, stderr, stdout)
).format(command, stderr, stdout)
def __str__(self):
"""Return a verbose error message indicating the command problem."""
lib/galaxy/util/path/__init__.py
+1 -2
View File
@@ -176,8 +176,7 @@ def safe_walk(path, allowlist=None):
if allowlist and i % WALK_MAX_DIRS == 0:
raise RuntimeError(
"Breaking out of walk of %r after %s iterations (most likely infinite symlink recursion) at: %r"
% (path, WALK_MAX_DIRS, dirpath)
f"Breaking out of walk of {path!r} after {WALK_MAX_DIRS} iterations (most likely infinite symlink recursion) at: {dirpath!r}"
)
_prefix = partial(join, dirpath)
lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+3 -5
View File
@@ -105,12 +105,10 @@ class AdminToolshed(AdminGalaxy):
repository = get_installed_tool_shed_repository(trans.app, repository_id)
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, str(repository.tool_shed))
if tool_shed_url is None or repository_name is None or repository_owner is None or changeset_revision is None:
message = "Unable to retrieve updated repository information from the Tool Shed because one or more of the following "
message += (
"required parameters is None: tool_shed_url: %s, repository_name: %s, repository_owner: %s, changeset_revision: %s "
% (str(tool_shed_url), str(repository_name), str(repository_owner), str(changeset_revision))
raise Exception(
"Unable to retrieve updated repository information from the Tool Shed because one or more of the following "
f"required parameters is None: tool_shed_url: {tool_shed_url}, repository_name: {repository_name}, repository_owner: {repository_owner}, changeset_revision: {changeset_revision} "
)
raise Exception(message)
params = dict(name=str(repository_name), owner=str(repository_owner), changeset_revision=changeset_revision)
pathspec = ["repository", "get_updated_repository_information"]
raw_text = util.url_get(
lib/galaxy/webapps/galaxy/controllers/dataset.py
+1 -2
View File
@@ -1092,8 +1092,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
if current_history in target_histories:
refresh_frames = ["history"]
hist_names_str = ", ".join(
'<a href="%s" target="_top">%s</a>'
% (
'<a href="{}" target="_top">{}</a>'.format(
url_for(
controller="history", action="switch_to_history", hist_id=trans.security.encode_id(hist.id)
),
lib/galaxy/webapps/galaxy/controllers/visualization.py
+3 -2
View File
@@ -476,8 +476,9 @@ class VisualizationController(
# Redirect to load galaxy frames.
return trans.show_ok_message(
message="""Visualization "%s" has been imported. <br>You can <a href="%s">start using this visualization</a> or %s."""
% (visualization.title, web.url_for("/visualizations/list"), referer_message),
message="""Visualization "{}" has been imported. <br>You can <a href="{}">start using this visualization</a> or {}.""".format(
visualization.title, web.url_for("/visualizations/list"), referer_message
),
use_panels=True,
)
lib/galaxy/webapps/galaxy/controllers/workflow.py
+3 -2
View File
@@ -301,8 +301,9 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
# Redirect to load galaxy frames.
return trans.show_ok_message(
message="""Workflow "%s" has been imported. <br>You can <a href="%s">start using this workflow</a> or %s."""
% (stored.name, web.url_for("/workflows/list"), referer_message)
message="""Workflow "{}" has been imported. <br>You can <a href="{}">start using this workflow</a> or {}.""".format(
stored.name, web.url_for("/workflows/list"), referer_message
)
)
@web.expose
lib/tool_shed/dependencies/repository/relation_builder.py
+14 -7
View File
@@ -263,21 +263,28 @@ class RelationBuilder:
# For backward compatibility to the 12/20/12 Galaxy release.
if len(components_list) in (4, 5):
rd_only_if_compiling_contained_td = "False"
message = (
log.debug(
"The revision %s defined for repository %s owned by %s is invalid, so repository "
% (str(rd_changeset_revision), str(rd_name), str(rd_owner))
"dependencies defined for repository %s will be ignored.",
rd_changeset_revision,
rd_name,
rd_owner,
repository_name,
)
message += f"dependencies defined for repository {repository_name} will be ignored."
log.debug(message)
else:
repository_components_tuple = container_util.get_components_from_key(key)
components_list = tool_shed.util.repository_util.extract_components_from_tuple(
repository_components_tuple
)
toolshed, repository_name, repository_owner, repository_changeset_revision = components_list[0:4]
message = f"The revision {rd_changeset_revision} defined for repository {rd_name} owned by {rd_owner} is invalid, "
message += f"so repository dependencies defined for repository {repository_name} will be ignored."
log.debug(message)
log.debug(
"The revision %s defined for repository %s owned by %s is invalid, "
"so repository dependencies defined for repository %s will be ignored.",
rd_changeset_revision,
rd_name,
rd_owner,
repository_name,
)
return updated_key_rd_dicts
def handle_circular_repository_dependency(self, repository_key, repository_dependency):
lib/tool_shed/grids/repository_grids.py
+6 -12
View File
@@ -859,14 +859,11 @@ class RepositoriesWithInvalidToolsGrid(RepositoryGrid):
invalid_tools = metadata.get("invalid_tools", [])
if invalid_tools:
for invalid_tool_config in invalid_tools:
href_str = (
'<a href="load_invalid_tool?repository_id=%s&tool_config=%s&changeset_revision=%s">%s</a>'
% (
trans.security.encode_id(repository.id),
invalid_tool_config,
repository_metadata.changeset_revision,
invalid_tool_config,
)
href_str = '<a href="load_invalid_tool?repository_id={}&tool_config={}&changeset_revision={}">{}</a>'.format(
trans.security.encode_id(repository.id),
invalid_tool_config,
repository_metadata.changeset_revision,
invalid_tool_config,
)
val += href_str
val += "<br/>"
@@ -1421,10 +1418,7 @@ class ValidRepositoryGrid(RepositoryGrid):
rval = "<ul>"
if repository.categories:
for rca in repository.categories:
rval += (
'<li><a href="browse_repositories?operation=valid_repositories_by_category&id=%s">%s</a></li>'
% (trans.security.encode_id(rca.category.id), rca.category.name)
)
rval += f'<li><a href="browse_repositories?operation=valid_repositories_by_category&id={trans.security.encode_id(rca.category.id)}">{rca.category.name}</a></li>'
else:
rval += "<li>not set</li>"
rval += "</ul>"
lib/tool_shed/metadata/repository_metadata_manager.py
+3 -2
View File
@@ -975,8 +975,9 @@ class RepositoryMetadataManager(metadata_generator.MetadataGenerator):
unsuccessful_count += 1
else:
log.debug(
"Successfully reset metadata on repository %s owned by %s"
% (str(repository.name), str(repository.user.username))
"Successfully reset metadata on repository %s owned by %s",
repository.name,
repository.user.username,
)
successful_count += 1
except Exception:
lib/tool_shed/util/metadata_util.py
+3 -2
View File
@@ -223,8 +223,9 @@ def get_repository_dependency_tups_from_repository_metadata(app, repository_meta
dependency_tups.append(repository_dependency_tup)
else:
log.debug(
"Cannot locate repository %s owned by %s for inclusion in repository dependency tups."
% (name, owner)
"Cannot locate repository %s owned by %s for inclusion in repository dependency tups.",
name,
owner,
)
return dependency_tups
lib/tool_shed/webapp/api/repositories.py
+12 -8
View File
@@ -262,8 +262,9 @@ class RepositoriesController(BaseAPIController):
return repository_dict, repository_metadata_dict, repo_info_dict
else:
log.debug(
"Unable to locate repository_metadata record for repository id %s and changeset_revision %s"
% (str(repository.id), str(changeset_revision))
"Unable to locate repository_metadata record for repository id %s and changeset_revision %s",
repository.id,
changeset_revision,
)
return repository_dict, {}, {}
else:
@@ -617,8 +618,9 @@ class RepositoriesController(BaseAPIController):
encoded_id = trans.security.encode_id(repository.id)
if encoded_id in encoded_ids_to_skip:
log.debug(
"Skipping repository with id %s because it is in encoded_ids_to_skip %s"
% (str(repository.id), str(encoded_ids_to_skip))
"Skipping repository with id %s because it is in encoded_ids_to_skip %s",
repository.id,
encoded_ids_to_skip,
)
elif repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION and repository.id not in handled_repository_ids:
results = handle_repository(trans, rmm, repository, results)
@@ -627,8 +629,9 @@ class RepositoriesController(BaseAPIController):
encoded_id = trans.security.encode_id(repository.id)
if encoded_id in encoded_ids_to_skip:
log.debug(
"Skipping repository with id %s because it is in encoded_ids_to_skip %s"
% (str(repository.id), str(encoded_ids_to_skip))
"Skipping repository with id %s because it is in encoded_ids_to_skip %s",
repository.id,
encoded_ids_to_skip,
)
elif repository.type != rt_util.TOOL_DEPENDENCY_DEFINITION and repository.id not in handled_repository_ids:
results = handle_repository(trans, rmm, repository, results)
@@ -811,8 +814,9 @@ class RepositoriesController(BaseAPIController):
return repository_metadata_dict
else:
log.debug(
"Unable to locate repository_metadata record for repository id %s and changeset_revision %s"
% (str(id), str(changeset))
"Unable to locate repository_metadata record for repository id %s and changeset_revision %s",
id,
changeset,
)
return {}
lib/tool_shed/webapp/api/repository_revisions.py
+7 -4
View File
@@ -199,15 +199,18 @@ class RepositoryRevisionsController(BaseAPIController):
# log information when setting attributes associated with the Tool Shed's install and test framework.
if key in ["includes_tools", "missing_test_components"]:
log.debug(
"Setting repository_metadata column %s to value %s for changeset_revision %s via the Tool Shed API."
% (str(key), str(new_value), str(repository_metadata.changeset_revision))
"Setting repository_metadata column %s to value %s for changeset_revision %s via the Tool Shed API.",
key,
new_value,
repository_metadata.changeset_revision,
)
setattr(repository_metadata, key, new_value)
flush_needed = True
if flush_needed:
log.debug(
"Updating repository_metadata record with id %s and changeset_revision %s."
% (str(decoded_repository_metadata_id), str(repository_metadata.changeset_revision))
"Updating repository_metadata record with id %s and changeset_revision %s.",
decoded_repository_metadata_id,
repository_metadata.changeset_revision,
)
trans.sa_session.add(repository_metadata)
trans.sa_session.flush()
lib/tool_shed/webapp/controllers/repository.py
+17 -17
View File
@@ -994,14 +994,13 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
self.install_matched_repository_grid.operations = operations
return self.install_matched_repository_grid(trans, **kwd)
else:
kwd["message"] = (
"tool id: <b>%s</b><br/>tool name: <b>%s</b><br/>tool version: <b>%s</b><br/>exact matches only: <b>%s</b>"
% (
basic_util.stringify(tool_ids),
escape(basic_util.stringify(tool_names)),
escape(basic_util.stringify(tool_versions)),
str(exact_matches_checked),
)
kwd[
"message"
] = "tool id: <b>{}</b><br/>tool name: <b>{}</b><br/>tool version: <b>{}</b><br/>exact matches only: <b>{}</b>".format(
basic_util.stringify(tool_ids),
escape(basic_util.stringify(tool_names)),
escape(basic_util.stringify(tool_versions)),
exact_matches_checked,
)
self.matched_repository_grid.title = "Repositories with matching tools"
return self.matched_repository_grid(trans, **kwd)
@@ -2292,8 +2291,9 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
return trans.response.send_redirect(web.url_for(controller="repository", action="index", user_id=user_id))
else:
return trans.show_error_message(
"The tool shed <b>%s</b> contains no repositories owned by <b>%s</b>."
% (web.url_for("/", qualified=True).rstrip("/"), str(owner))
"The tool shed <b>{}</b> contains no repositories owned by <b>{}</b>.".format(
web.url_for("/", qualified=True).rstrip("/"), owner
)
)
@web.expose
@@ -2316,7 +2316,9 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
user = None
if user:
user_id = trans.security.encode_id(user.id)
message = f"This list of repositories owned by <b>{str(owner)}</b>, does not include one named <b>{str(name)}</b>."
message = (
f"This list of repositories owned by <b>{owner}</b>, does not include one named <b>{name}</b>."
)
return trans.response.send_redirect(
web.url_for(
controller="repository", action="index", user_id=user_id, message=message, status="error"
@@ -2324,8 +2326,9 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
)
else:
return trans.show_error_message(
"The tool shed <b>%s</b> contains no repositories named <b>%s</b> with owner <b>%s</b>."
% (web.url_for("/", qualified=True).rstrip("/"), str(name), str(owner))
"The tool shed <b>{}</b> contains no repositories named <b>{}</b> with owner <b>{}</b>.".format(
web.url_for("/", qualified=True).rstrip("/"), name, owner
)
)
@web.expose
@@ -2360,10 +2363,7 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
)
)
else:
message = (
"The change log for the repository named <b>%s</b> owned by <b>%s</b> does not include revision <b>%s</b>."
% (escape(str(name)), escape(str(owner)), escape(str(changeset_revision)))
)
message = f"The change log for the repository named <b>{escape(str(name))}</b> owned by <b>{escape(str(owner))}</b> does not include revision <b>{escape(str(changeset_revision))}</b>."
return trans.response.send_redirect(
web.url_for(
controller="repository",
lib/tool_shed/webapp/framework/decorators.py
+3 -2
View File
@@ -14,8 +14,9 @@ def require_login(verb="perform this action", use_panels=False):
return func(self, trans, *args, **kwargs)
else:
return trans.show_error_message(
'You must be <a target="galaxy_main" href="%s">logged in</a> to %s.'
% (url_for(controller="user", action="login"), verb),
'You must be <a target="galaxy_main" href="{}">logged in</a> to {}.'.format(
url_for(controller="user", action="login"), verb
),
use_panels=use_panels,
)
lib/tool_shed/webapp/model/__init__.py
+1 -2
View File
@@ -438,8 +438,7 @@ class Repository(Base, Dictifiable):
if str(role.name) == admin_role_name:
return role
raise Exception(
"Repository %s owned by %s is not associated with a required administrative role."
% (str(self.name), str(self.user.username))
f"Repository {self.name} owned by {self.user.username} is not associated with a required administrative role."
)
def allow_push(self):